Input and runtime details for job 6860187 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation	Additional homologs
81	0.008673	0.3575	b1683	sufB	-9.84	0.294156	211 -- 257	124 -- 171	component of SufBCD Fe-S cluster assembly scaffold		_____________210_______________258\n_____________\|_________________\|\n5'-GUU...AAUCA________AAUU_____ACCCU...AGC-3'\n______________GAUAUUCA____UCACA\n______________:\|\|\|:\|\|\|____\|\|\|\|\|\n______________UUAUGAGU____AGUGU\n3'-UUU...UGUGG________C________GUACU...UAG-5'\n_____________\|_________________\|\n_____________172_______________123\n	127 -- 133	175 -- 181	-8.93573 kcal/mol	1.46068 kcal/mol	0.409577 kcal/mol	210 258@LB@ \| \|@LB@5'-GUU...AAUCA AAUU ACCCU...AGC-3'@LB@ GAUAUUCA UCACA@LB@ :\|\|\|:\|\|\| \|\|\|\|\|@LB@ UUAUGAGU AGUGU@LB@3'-UUU...UGUGG C GUACU...UAG-5'@LB@ \| \|@LB@ 172 123@LB@@LB@@LB@Energy -9.84 kcal/mol@LB@Hybridization Energy -8.93573 kcal/mol@LB@Unfolding Energy - mRNA 1.46068 kcal/mol@LB@Unfolding Energy - sRNA 0.409577 kcal/mol@LB@@LB@Position - mRNA 211 -- 257@LB@Position - sRNA 124 -- 171@LB@Position Seed - mRNA 127 -- 133@LB@Position Seed - sRNA 175 -- 181@LB@
182	0.02094	0.3833	b0248	yafX	-12.67	0.081205	189 -- 235	52 -- 92	CP4-6 prophage; uncharacterized protein	b2643	_____________188______________________236\n_____________\|________________________\|\n5'-CCG...ACACA___G_________C____ACC___UAACC...GGC-3'\n______________GAC_CAGCACGAC_UCGC___CGC\n______________:\|\|_\|\|\|\|\|\|:\|\|_\|\|\|\|___\|\|\|\n______________UUG_GUCGUGUUG_AGCG___GCG\n3'-UUU...UUGCG_____________A____ACA___CCAUU...UAG-5'\n_____________\|________________________\|\n_____________93_______________________51\n	218 -- 224	63 -- 69	-27.2596 kcal/mol	3.0161 kcal/mol	15.5954 kcal/mol	188 236@LB@ \| \|@LB@5'-CCG...ACACA G C ACC UAACC...GGC-3'@LB@ GAC CAGCACGAC UCGC CGC@LB@ :\|\| \|\|\|\|\|\|:\|\| \|\|\|\| \|\|\|@LB@ UUG GUCGUGUUG AGCG GCG@LB@3'-UUU...UUGCG A ACA CCAUU...UAG-5'@LB@ \| \|@LB@ 93 51@LB@@LB@@LB@Energy -12.67 kcal/mol@LB@Hybridization Energy -27.2596 kcal/mol@LB@Unfolding Energy - mRNA 3.0161 kcal/mol@LB@Unfolding Energy - sRNA 15.5954 kcal/mol@LB@@LB@Position - mRNA 189 -- 235@LB@Position - sRNA 52 -- 92@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 63 -- 69@LB@
47	0.004619	0.3205	b4142	groS	-15.85	0.018169	259 -- 271	196 -- 208	Cpn10 chaperonin GroES small subunit of GroESL		_____________258_______________________________272\n_____________\|_________________________________\|\n5'-UGA...AACUA_____________CAUCGUUCUG__________UGCAG...CUA-3'\n______________AAUCUGCUGGCGG__________ACCG__GCUC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|__________\|\|\|:__:\|\|\|\n______________UUAGACGACCGCC__________UGGU__UGAG\n3'-UUU...CCAUA_____________CACUAAAAUG____UA____UCAGU...UAG-5'\n_____________\|_________________________________\|\n_____________209_______________________________195\n	265 -- 271	196 -- 202	-33.1058 kcal/mol	10.148 kcal/mol	14.8106 kcal/mol	258 272@LB@ \| \|@LB@5'-UGA...AACUA CAUCGUUCUG UGCAG...CUA-3'@LB@ AAUCUGCUGGCGG ACCG GCUC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|: :\|\|\|@LB@ UUAGACGACCGCC UGGU UGAG@LB@3'-UUU...CCAUA CACUAAAAUG UA UCAGU...UAG-5'@LB@ \| \|@LB@ 209 195@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -33.1058 kcal/mol@LB@Unfolding Energy - mRNA 10.148 kcal/mol@LB@Unfolding Energy - sRNA 14.8106 kcal/mol@LB@@LB@Position - mRNA 259 -- 271@LB@Position - sRNA 196 -- 208@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 196 -- 202@LB@
106	0.01145	0.3575	b2350	gtrA	-11.86	0.119007	4 -- 25	148 -- 167	CPS-53 (KpLE1) prophage; bactoprenol-linked glucose translocase/flippase		_____________3_____________26\n_____________\|_____________\|\n5'-GAA...UGUAU__AU_________ACAAACC-3'\n______________CU__GUCGCGCAU\n______________\|\|__\|\|\|:\|:\|\|\|\n______________GA__CAGUGUGUA\n3'-UUU...GUUAU__GU_________CUACG...UAG-5'\n_____________\|_____________\|\n_____________168___________147\n	287 -- 293	166 -- 172	-13.6011 kcal/mol	2.0532 kcal/mol	0.604639 kcal/mol	3 26@LB@ \| \|@LB@5'-GAA...UGUAU AU ACAAACC-3'@LB@ CU GUCGCGCAU@LB@ \|\| \|\|\|:\|:\|\|\|@LB@ GA CAGUGUGUA@LB@3'-UUU...GUUAU GU CUACG...UAG-5'@LB@ \| \|@LB@ 168 147@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -13.6011 kcal/mol@LB@Unfolding Energy - mRNA 2.0532 kcal/mol@LB@Unfolding Energy - sRNA 0.604639 kcal/mol@LB@@LB@Position - mRNA 4 -- 25@LB@Position - sRNA 148 -- 167@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 166 -- 172@LB@
151	0.01691	0.3749	b2442	intZ	-12.49	0.088679	278 -- 291	17 -- 31	CPZ-55 prophage; putative phage integrase	b2349	_____________277_________________292\n_____________\|___________________\|\n5'-ACA...AAACU____________C_G____CGGGG...UGC-3'\n______________CACCGAU__UCA_U_ACGC\n______________\|\|\|\|:\|\|__\|\|\|_\|_\|\|:\|\n______________GUGGUUA__AGU_A_UGUG\n3'-UUU...AAAAU_______UG___C_G____UACUA...UAG-5'\n_____________\|___________________\|\n_____________32__________________16\n	269 -- 275	180 -- 186	-14.1411 kcal/mol	1.5591 kcal/mol	4.88042 kcal/mol	277 292@LB@ \| \|@LB@5'-ACA...AAACU C G CGGGG...UGC-3'@LB@ CACCGAU UCA U ACGC@LB@ \|\|\|\|:\|\| \|\|\| \| \|\|:\|@LB@ GUGGUUA AGU A UGUG@LB@3'-UUU...AAAAU UG C G UACUA...UAG-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -12.49 kcal/mol@LB@Hybridization Energy -14.1411 kcal/mol@LB@Unfolding Energy - mRNA 1.5591 kcal/mol@LB@Unfolding Energy - sRNA 4.88042 kcal/mol@LB@@LB@Position - mRNA 278 -- 291@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 180 -- 186@LB@
190	0.02217	0.3833	b2754	ygbF	-10.33	0.238061	176 -- 225	124 -- 165	CRISPR adaptation ssRNA endonuclease		_____________175____________226\n_____________\|______________\|\n5'-UGG...AAAAU________GC____ACGAG...GUG-3'\n______________GUACCUCC__GCUU\n______________\|:\|\|\|:\|\|__\|\|\|\|\n______________CGUGGGGG__CGAA\n3'-UUU...UACCC________AA____GUAG-5'\n_____________\|______________\|\n_____________166____________123\n	232 -- 238	11 -- 17	-17.8256 kcal/mol	3.33543 kcal/mol	6.90657 kcal/mol	175 226@LB@ \| \|@LB@5'-UGG...AAAAU GC ACGAG...GUG-3'@LB@ GUACCUCC GCUU@LB@ \|:\|\|\|:\|\| \|\|\|\|@LB@ CGUGGGGG CGAA@LB@3'-UUU...UACCC AA GUAG-5'@LB@ \| \|@LB@ 166 123@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -17.8256 kcal/mol@LB@Unfolding Energy - mRNA 3.33543 kcal/mol@LB@Unfolding Energy - sRNA 6.90657 kcal/mol@LB@@LB@Position - mRNA 176 -- 225@LB@Position - sRNA 124 -- 165@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 11 -- 17@LB@
27	0.002233	0.2633	b3525	yhjH	-10.03	0.271118	185 -- 216	151 -- 171	cyclic-di-GMP phosphodiesterase FlhDC-regulated		_____________184_______________________________217\n_____________\|_________________________________\|\n5'-UUA...UUUAA__A___G_____CUU_____AUA__________UCCAG...CCU-3'\n______________AC_CAG__ACAU___UGAUG___AGGCAGGUUA\n______________\|\|_\|\|\|__\|\|\|:___\|\|\|\|\|___\|\|\|\|\|:\|\|:\|\n______________UG_GUC__UGUG___ACUAC___UCCGUUCAGU\n3'-UUU...GGUUA__A___AG____U_______G____________UGAAA...UAG-5'\n_____________\|_________________________________\|\n_____________172_______________________________150\n	209 -- 215	152 -- 158	-24.6278 kcal/mol	4.97701 kcal/mol	8.14531 kcal/mol	184 217@LB@ \| \|@LB@5'-UUA...UUUAA A G CUU AUA UCCAG...CCU-3'@LB@ AC CAG ACAU UGAUG AGGCAGGUUA@LB@ \|\| \|\|\| \|\|\|: \|\|\|\|\| \|\|\|\|\|:\|\|:\|@LB@ UG GUC UGUG ACUAC UCCGUUCAGU@LB@3'-UUU...GGUUA A AG U G UGAAA...UAG-5'@LB@ \| \|@LB@ 172 150@LB@@LB@@LB@Energy -10.03 kcal/mol@LB@Hybridization Energy -24.6278 kcal/mol@LB@Unfolding Energy - mRNA 4.97701 kcal/mol@LB@Unfolding Energy - sRNA 8.14531 kcal/mol@LB@@LB@Position - mRNA 185 -- 216@LB@Position - sRNA 151 -- 171@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 152 -- 158@LB@
78	0.008099	0.3458	b2810	csdA	-12.29	0.097398	132 -- 155	3 -- 23	cysteine sulfinate desulfinase		_____________131_______________156\n_____________\|_________________\|\n5'-CUU...GGUUA____U________A___AAGUG...AAG-3'\n______________GCAC_CUCCUUGU_UCA\n______________\|\|\|\|_\|:\|\|\|\|\|:_\|\|\|\n______________CGUG_GGGGAACG_AGU\n3'-UUU...UACCC_____________A___AG-5'\n_____________\|_________________\|\n_____________24________________2\n	145 -- 151	7 -- 13	-20.4088 kcal/mol	3.04417 kcal/mol	7.17675 kcal/mol	131 156@LB@ \| \|@LB@5'-CUU...GGUUA U A AAGUG...AAG-3'@LB@ GCAC CUCCUUGU UCA@LB@ \|\|\|\| \|:\|\|\|\|\|: \|\|\|@LB@ CGUG GGGGAACG AGU@LB@3'-UUU...UACCC A AG-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -12.29 kcal/mol@LB@Hybridization Energy -20.4088 kcal/mol@LB@Unfolding Energy - mRNA 3.04417 kcal/mol@LB@Unfolding Energy - sRNA 7.17675 kcal/mol@LB@@LB@Position - mRNA 132 -- 155@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 7 -- 13@LB@
67	0.006568	0.3261	b1927	amyA	-8.95	0.423898	77 -- 95	58 -- 76	cytoplasmic alpha-amylase		_____________76_____________________96\n_____________\|______________________\|\n5'-UUA...GAAAC__G_______GU___C______AAAAU...AUA-3'\n______________UG_UCGGUCA__CAU_GGUGCA\n______________\|:_\|\|:\|\|\|\|__\|\|\|_\|:\|\|\|\|\n______________AU_AGUCAGU__GUA_CUACGU\n3'-UUU...UGGUU__G_______GU__________CCGUU...UAG-5'\n_____________\|______________________\|\n_____________77_____________________57\n	35 -- 41	171 -- 177	-21.7732 kcal/mol	10.1812 kcal/mol	4.80336 kcal/mol	76 96@LB@ \| \|@LB@5'-UUA...GAAAC G GU C AAAAU...AUA-3'@LB@ UG UCGGUCA CAU GGUGCA@LB@ \|: \|\|:\|\|\|\| \|\|\| \|:\|\|\|\|@LB@ AU AGUCAGU GUA CUACGU@LB@3'-UUU...UGGUU G GU CCGUU...UAG-5'@LB@ \| \|@LB@ 77 57@LB@@LB@@LB@Energy -8.95 kcal/mol@LB@Hybridization Energy -21.7732 kcal/mol@LB@Unfolding Energy - mRNA 10.1812 kcal/mol@LB@Unfolding Energy - sRNA 4.80336 kcal/mol@LB@@LB@Position - mRNA 77 -- 95@LB@Position - sRNA 58 -- 76@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 171 -- 177@LB@
122	0.01342	0.3575	b4087	alsA	-13.14	0.065197	11 -- 23	124 -- 136	D-allose ABC transporter ATPase		_____________10___________24\n_____________\|____________\|\n5'-AAU...GGCAA____________GGAUA...UAC-3'\n______________GGUUAUCCCGCU\n______________\|\|\|:\|\|\|\|\|:\|\|\n______________CCAGUAGGGUGA\n3'-UUU...UAACG____________CGUAG...UAG-5'\n_____________\|____________\|\n_____________137__________123\n	16 -- 22	125 -- 131	-19.4238 kcal/mol	3.3353 kcal/mol	6.53419 kcal/mol	10 24@LB@ \| \|@LB@5'-AAU...GGCAA GGAUA...UAC-3'@LB@ GGUUAUCCCGCU@LB@ \|\|\|:\|\|\|\|\|:\|\|@LB@ CCAGUAGGGUGA@LB@3'-UUU...UAACG CGUAG...UAG-5'@LB@ \| \|@LB@ 137 123@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -19.4238 kcal/mol@LB@Unfolding Energy - mRNA 3.3353 kcal/mol@LB@Unfolding Energy - sRNA 6.53419 kcal/mol@LB@@LB@Position - mRNA 11 -- 23@LB@Position - sRNA 124 -- 136@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 125 -- 131@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

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When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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